What Causes Irrigation Line Clogs? Monitoring & Maintenance Best Practices

What Causes Irrigation Line Clogs? Monitoring & Maintenance Best Practices

A guide to irrigation system clogs in cultivation - their causes and effective solutions. Learn how to prevent, identify, and address blockages through best practices in water treatment, nutrient management, irrigation system design, monitoring, maintenance and more. 3 case studies included!
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Irrigation system problems are among the most common and costly issues faced by cultivators, leading to damage to crop health, reduced yields, and high labor costs for emergency repairs and replacements.

While hydroponic irrigation systems vary in design, this article focuses on the common issues found in precision drip systems (PDS), which are widely used in commercial controlled environment agriculture (CEA). These systems typically include mainline supply pipes, distribution lines, and small-diameter delivery tubes with emitters at each plant.

Proper flow in irrigation systems is essential for several key reasons:

  1. Nutrient delivery: Adequate flow ensures that all plants receive the necessary nutrients in the right proportions. Uneven distribution due to clogs can lead to nutrient deficiencies and imbalances.
  2. Oxygen availability: As the nutrient solution circulates, it oxygenates the root zone. Clogs can cause stagnant areas, leading to hypoxia (lack of oxygen), which hinders root respiration and nutrient uptake.
  3. Temperature control: Consistent flow helps regulate the temperature of the nutrient solution. Stagnant water can lead to temperature fluctuations, which can stress plants and promote algae growth.
  4. Waste removal: Proper flow helps remove metabolic waste products and prevents the accumulation of toxic substances in the root zone.
  5. System longevity: Clogs can cause undue stress on pumps, leading to premature failure. Maintaining proper flow ensures the system works efficiently and extends equipment life.
  6. Labor savings: Dealing with clogs and poor irrigation uniformity impacts labor costs and reduces the labor availability for crop care.

Proper functioning of irrigation systems is required for optimal plant growth, nutrient uptake, and overall system health. Clogs disrupt flow, causing issues that negatively affect plant performance and system longevity. Beyond that, cultivators cannot effectively implement advanced irrigation techniques for comprehensive crop steering without uniform water/fertilizer delivery and consistent substrate conditions.

In the following sections, we will explore strategies and solutions to help cultivators address these common irrigation issues, ensuring optimal system performance and crop health.

Types of Clogs

As a cultivator, you may encounter three main types of clogs in your irrigation system: physical, chemical, and biological. Understanding the differences between these clogs is key for effectively addressing and preventing them.


Physical clogs are caused by suspended particles in the source or irrigation water. Sources of these particles include sand and other suspended debris that are too large to pump through the channels of drip emitters. These are the least common in hydroponic systems where source water is already quite clean (municipal) and easily ensured with basic sediment filters.


Emitter blockages often occur from chemical reactions due to the buildup of minerals like calcium, magnesium, iron, or manganese. These minerals form deposits that can obstruct water flow. High pH water, above 7, with considerable mineral content is prone to causing such clogs. Calcium carbonate deposits are especially likely to form in higher pH and temperature conditions, as calcium's solubility decreases under these circumstances.

  1. Calcium deposits: Calcium is an essential nutrient for plant growth, but when present in high concentrations, it can precipitate out of solution and form solid deposits. These deposits, often referred to as calcium carbonate or limescale, can accumulate in pipes, emitters, and other system components, causing clogs.
  2. Iron deposits: Similar to calcium, iron can also precipitate out of solution and form deposits that clog the system. Iron buildup is more common in systems with high iron concentrations or pH imbalances.
  3. Other mineral accumulations: Depending on the water source and nutrient formulation, other minerals such as magnesium, sulfur, and phosphate can also contribute to clog formation.

Shi, K.; Lu, T.; Zheng, W.; Zhang, X.; Zhangzhong, L. A Review of the Category, Mechanism, and Controlling Methods of Chemical Clogging in Drip Irrigation System. Agriculture 202212, 202. https://doi.org/10.3390/agriculture12020202


Organic matter clogs are caused by the growth and accumulation of algae and bacteria within the irrigation system. These microorganisms thrive in moist, nutrient-rich environments and can quickly multiply, forming thick biofilms that obstruct water flow. The biofilms increase the viscosity of the emitter/tubing wall, causing suspended minerals and particulates to aggregate there. Water sources rich in nutrients, such as hydroponic fertilizer, have greater potential to support bacterial growth. Many bacteria can oxidize iron, manganese, or other metals/minerals in the irrigation water and form biofilms inside irrigation components.

Causes of Clogs

There are a number of factors that influence the likelihood and degree of clogging in irrigation systems. Let’s look at some of these:

Poor water quality:

  1. High mineral content: Water sources with high levels of minerals, such as calcium, magnesium, and iron, can lead to mineral buildup and clog formation in hydroponic systems. As water evaporates from the system, the concentration of these minerals increases, exacerbating the problem.
  2. Contaminated water sources: Water contaminated with organic matter, such as bacteria, fungi, or algae spores, can introduce these organisms into the hydroponic system. As these contaminants grow and multiply, they can form clogs and obstruct water flow.

Inadequate filtration:

  1. Improper filter sizing: Filters are essential for removing debris and contaminants from the nutrient solution. However, if the filters are undersized or not suitable for the specific needs of the system, they can become overwhelmed and fail to effectively remove particles, leading to clogs.
  2. Infrequent filter maintenance: Even with properly sized filters, regular maintenance is crucial. If filters are not cleaned or replaced on a regular basis, they can become clogged themselves, reducing their effectiveness and causing clogs downstream in the system.

System design flaws:

  1. Insufficient pipe diameter: If pipes are too narrow, they can restrict water flow and increase the likelihood of clogs. This is especially true in systems with high flow rates or long pipe runs.
  2. Low water pressure: Inadequate water pressure can lead to slow flow rates and stagnant areas in the system, encouraging the accumulation of debris and the growth of algae and other clog-forming organisms.

Environmental factors:

  1. High temperatures: Warm water temperatures can accelerate the growth of algae and other microorganisms, increasing the risk of clogs. High ambient temperatures can also cause mineral precipitates to form more readily.
  2. Dust and debris accumulation: In indoor growing environments, dust and debris from fans, ventilation systems, and human activity can settle into the hydroponic system, contributing to clog formation.
  3. Microbial load: High levels of bacteria, fungi, and algae in the source water or air can lead to the formation of biofilms and slime, which can adhere to surfaces and accumulate in narrow passages, causing clogs. These microorganisms thrive in warm, nutrient-rich environments and can be introduced through contaminated water sources, infected plants, or poor sanitation practices.

Normal usage:

  1. Even with diligent maintenance, thoughtful system design, and adherence to usage protocols, clogs are still likely to occur in precision drip systems during normal operation. The levels of nutrient concentration typically needed for commercial cultivation - which often exceed 3EC - pose a risk of causing harmful reactions over time.

Preventing Clogs in Hydroponic Systems

As a cultivator, it's essential to understand the various factors that contribute to the formation of clogs in your irrigation system. By recognizing these causes, you can take proactive measures to prevent clogs and maintain optimal system performance. Let's explore some of the key factors:

Proper system design:

  1. Adequate pipe sizing: When designing a hydroponic system, it is crucial to select pipes with sufficient diameter to accommodate the desired flow rates without creating excessive pressure or restricting flow. Larger pipes can help reduce the risk of clogs by allowing debris to pass through more easily.
  2. Sufficient water pressure: Ensuring adequate water pressure throughout the system helps maintain proper flow rates and prevents stagnant areas where clogs can form. This can be achieved through the use of appropriately sized pumps and well-designed plumbing layouts.
  3. Proper drainage and flush valves: Incorporating proper flush points into the system design allows for the complete removal of suspended materials, without forcing these materials through the emitters.
  4. Quality emitter selection: We generally prefer Rivulis or Netafim pressure-compensating emitters. These emitters will provide very uniform flow rate across their pressure range, however like all precision drip emitters, are susceptible to clogging due to the narrow flow path. Using emitters with a higher minimum opening pressure allows the grower to flush the system without pushing solution through the emitter itself.

Regular maintenance:

  1. Filter cleaning and replacement: Regular cleaning and replacement of filters is essential to prevent clogs. The frequency of filter maintenance will depend on the specific system and water quality, but a general rule is to clean filters whenever there is a noticeable decrease in flow rate or increase in pressure. Filters should be replaced as recommended by the manufacturer.
  2. Flushing lines: Periodically flushing the entire hydroponic system can help remove accumulated debris and prevent clog formation. This involves running a high volume of water through the system to dislodge and flush out any buildup.
  3. Cleaning sensors and emitters: Sensors and emitters can become clogged over time, leading to inaccurate readings and uneven nutrient distribution. Regular cleaning of these components helps maintain their accuracy and efficiency.
  4. Post-Harvest Maintenance: The period of time post-harvest when plants are removed from the room is the best time to use higher intensity cleaning methods. The standard practice that we use here involves an acid injection (e.g. Green Clean Acid) to dissolve mineral buildup followed by high concentration sanitation (e.g. Sanidate or Calcium Hypochlorite). A key component of this process is flushing the dissolved/dislodged materials out through the flush valves and not through the emitters themselves.
  5. Annual Replacement: Given the high cost of clogs and poor uniformity on plant health and yield versus the low cost of emitter components, most facilities will create significant net gains from annually replacing all of their emitters and on-table irrigation components.

Water treatment:

We’ve discussed water treatment extensively in some of our other posts on Water Cleanliness, but here is a quick overview of some common solutions:

  1. Reverse osmosis: Reverse osmosis (RO) is a water purification process that removes dissolved minerals, bacteria, and other contaminants from the water supply. Using RO-treated water in hydroponic systems can help prevent mineral buildup and reduce the risk of clogs.
  2. UV sterilization: Ultraviolet (UV) sterilization involves exposing the water supply to UV light, which kills bacteria, viruses, and other microorganisms. This can help prevent the growth of algae and other clog-forming organisms in the hydroponic system.
  3. Water softening: For water sources with high mineral content where RO filtration isn’t a viable strategy, water softening can be an effective solution. Water softeners remove excess calcium and magnesium ions from the water, reducing the risk of mineral buildup and clog formation.
  4. Oxidizers: This is one particular method that we strongly recommend against. Oxidizers, especially hydrogen peroxide and other peroxide compounds, can oxidize the high concentration of metals that exist within Front Row Ag and other fertilizers, causing an acute increase in turbidity. While turbidity itself does not increase the risk of system clogs, it does increase cleaning demands for tanks where oxidizes minerals can accumulate on the sides.
  5. Chlorine compounds: As bacterial action in source water is one of the most common causes of system clogs, keeping irrigation water clean is one of the highest-leverage ways of preventing this. For this, we recommend using Calcium Hypochlorite at a rate that maintains an ORP of 300-500mV or chlorine level of 2ppm at the dripper.

Nutrient management:

Here we come to some of the specific factors that relate to fertilizers formulation and pH. We’ve discussed some of these factors before here and here, but lets quickly review:

  1. Balanced nutrient solutions: Using well-balanced nutrient solutions tailored to the specific needs of the plants can help prevent mineral buildup and clog formation. Avoid using excessive concentrations of nutrients, as this can lead to precipitation and accumulation in the system. Favor high-purity, acidic, fertilizers that enhance solubility within the solution, like Front Row Ag.
  2. pH control: Maintaining the proper pH range in the nutrient solution is crucial for preventing clogs. Some minerals, such as calcium and phosphate, are more likely to precipitate out of solution at higher pH levels. Regularly monitoring and adjusting pH can help keep these minerals in solution and prevent clog formation. Especially important here is the type, concentration (proper dilution is key), and injection order of pH up products. Applying pH up products at the start of the fertilizer panel raises the pH of the downstream solution as it hits the subsequent fertilizer injectors. Since mineral are less soluble at higher pH levels, this can lead to precipitations and potential clogs in filters and emitters.

Detecting and Diagnosing Clogs

Visual inspection:

  1. Checking for visible signs: One of the simplest ways to detect clogs is through visual inspection of the hydroponic system. This involves checking pipes, pumps, injectors, emitters, and other components for visible obstructions, such as algae buildup, root mass, or accumulated debris. It’s also important to check water storage tanks as our commercial reps often find excessive biofilms have accumulated in RO or other “clean” water storage tanks. Additionally, early stage biofilm accumulation may be more evident on filters, membranes, and disc filters; these should be routinely inspected for early detection of problems. Regularly inspecting the system can help identify potential clog issues before they become severe.
  2. Observing plant health: Clogs can cause uneven nutrient distribution and water stress, which can manifest as visible symptoms in the plants. Regularly observing plant health can provide early indications of clog issues. Signs to look for include wilting, yellowing or discolored leaves, stunted growth, and uneven growth patterns among plants in the same system.

Monitoring system performance:

  1. Pressure gauges: Installing pressure gauges at key points in the hydroponic system can help detect clogs by monitoring changes in water pressure. A sudden increase in pressure can indicate a clog restricting water flow, while a decrease in pressure may suggest a leak or a failing pump. Installing pressure gauges on the high and low side of your filters allows for an easily viewable indicator of slowly accumulating filter obstruction.
  2. Flow meters: Flow meters measure the rate of water flow through the system. A decrease in flow rate can indicate a clog impeding water movement. By regularly monitoring flow rates and comparing them to baseline values, growers can quickly identify potential clog issues.
  3. Substrate sensors: With high-tech substrate monitoring made possible by systems like AROYA, more growers are monitoring WC% and substrate EC on a daily basis. This is one of the best ways to detect clogs in irrigation: noticing an acute deviation or steep trend (without any planned changes in irrigation programming) in the pattern of WC or EC on the monitoring charts can be a strong warning signal that clogs are developing.
  4. Feed and runoff collection: Manual monitoring of feed and runoff volumes is a key part of optimizing performance in cultivation for a variety of reasons, including detection of irrigation problems. Growers should be calculating both the total daily irrigation volume per room and per plant. If the flow volume for the room is below the calculated target, or the volume of feed captured in the zone feed cup is below target, it’s a clear sign that something warrants further investigation.
  5. Stock tank utilization: When using the “Stack” recipe with the 3-2-2 Stock Mixing, the A, B, and Bloom stock tanks should be drawn down in exactly equal ratios - if they’re not, it is a clear indicator that there is issues on the injection side.

When diagnosing clogs, it's essential to consider the location and nature of the issue. Clogs can occur in different parts of the system, such as in the main water lines, individual feeder lines, or at the emitters. The type of clog (e.g., mineral buildup, organic matter, or physical particles) can also influence the diagnosis and the appropriate course of action.

To diagnose the cause of a clog, growers should consider factors such as:

  • The age of the system and its components
  • The quality of the water source
  • The composition of the nutrient solution
  • Recent changes to the system or maintenance routines
  • Environmental conditions, such as temperature and humidity

By combining visual inspection and system performance monitoring, hydroponic growers can effectively detect and diagnose clogs, allowing for timely intervention and minimizing the impact on plant health and system efficiency.

Clearing and Repairing Clogs

Manual removal:

  1. Disassembling and cleaning components: For accessible clogs, manual removal can be an effective solution. This involves disassembling the affected components, such as pipes, pumps, or emitters, and physically removing the obstruction. Cleaning the components with a brush or a high-pressure water jet can help dislodge the clog material.

Chemical or biological treatments:

  1. Acid injection for mineral buildup: For clogs caused by mineral buildup, such as calcium carbonate or iron deposits, acid injection can be an effective treatment. This involves introducing a mild acid solution, such as Biosafe Green Clean Acid, into the affected area to dissolve the mineral deposits. Follow the manufacturer's instructions and take proper safety precautions when using acid treatments.
  2. Enzyme treatments for organic matter: Clogs caused by organic matter, such as algae or biofilm, can be treated with enzyme-based products. These enzymes break down the organic material, making it easier to flush out of the system. Enzyme treatments are generally safer and more environmentally friendly than harsh chemical treatments. They can also eat away clogs that have formed deep inside emitter components in a way that is not possible with oxidizing agents. Front Row Ag Bioflo is one such example of enzymatic cleaning product with robust activity on the types of biofilms that can develop in hydroponic components, while being safe for use with plants.

Replacing damaged components: In some cases, clogs may cause permanent damage to system components, such as cracked pipes or worn-out pumps. In these situations, the best course of action may be to replace the damaged components entirely. When replacing components, it's essential to choose high-quality, clog-resistant options and ensure proper installation to prevent future issues.

When clearing and repairing clogs, take a systematic approach and address the root cause of the problem. After removing the clog, growers should thoroughly flush the system to remove any remaining debris and ensure proper flow is restored. It's also essential to review and adjust maintenance routines, nutrient management, and environmental controls to prevent the recurrence of clogs.

In cases where clogs are severe or persistent, it may be necessary to seek the assistance of a professional hydroponic system technician. These experts can provide specialized tools, knowledge, and experience to effectively clear clogs and repair damage while minimizing disruption to the growing operation.

Case Studies:

Here are some example case studies of common irrigation problems, as well as how they were detected and addressed.

Case Study 1: Eliminating Bacterial Clogs with Calcium Hypochlorite Injection

The Problem

A hydroponic grower noticed a gradual decline in system performance, with reduced flow rates and uneven nutrient distribution. Upon visual inspection, the grower discovered significant biofilm accumulation in the water storage tanks, despite using RO-filtered water. The presence of bacteria in the holding tanks was causing clogs in the irrigation lines and emitters, leading to suboptimal plant health and yields.

The Solution

To address the bacterial contamination issue, the grower implemented a calcium hypochlorite injection system before the RO storage tank. By continuously dosing the water with a low concentration of chlorine, the grower was able to maintain a stable ORP (oxidation-reduction potential) level between 300-500 mV and a free chlorine concentration of 2 ppm at the emitters.

The calcium hypochlorite injection effectively eliminated the bacterial growth in the water storage tanks and prevented the formation of biofilms. As a result, the grower observed a significant reduction in clog occurrence and improved overall system performance.

The Outcome

By proactively addressing the root cause of the bacterial clogs, the grower was able to:

  1. Restore proper flow rates and uniform nutrient distribution throughout the system
  2. Improve plant health and yield, as the plants received consistent access to water and nutrients
  3. Reduce labor costs associated with frequent system maintenance and cleaning
  4. Extend the life of the irrigation components by minimizing the damaging effects of biofilm accumulation

Case Study 2: Preventing Precipitation Clogs through pH Management

The Problem

A hydroponic grower experienced frequent clogging issues in the irrigation system, particularly at the emitters. Upon investigation, the grower discovered that the clogs were caused by mineral precipitates, primarily calcium. The precipitation was occurring due to the high pH of the nutrient solution, which reduced the solubility of certain minerals.

The grower had been using excessive amounts of pH-up products at the beginning of the fertilizer injection process, causing the pH to rise above the optimal range. As a result, minerals were precipitating out of solution and accumulating in the irrigation lines and emitters.

The Solution

To address the precipitation issue, the grower implemented a more efficient pH management strategy:

  1. The injection order was adjusted, with pH-up products added last in the fertilizer injection sequence. This prevented the pH from rising too early and affecting the solubility of the other nutrients.
  2. The concentration of pH-up products was carefully monitored and adjusted to maintain the nutrient solution pH within the optimal range (5.5-6.5) for crop growth. This range also promoted better mineral solubility and reduced the risk of precipitation.
  3. The grower installed pH sensors at key points in the irrigation system to continuously monitor pH levels and make real-time adjustments as needed.

By optimizing the pH management practices, the grower successfully minimized the occurrence of mineral precipitates and reduced the frequency of emitter clogs.

The Outcome

The implementation of better pH management techniques led to several positive outcomes:

  1. Reduced clogging incidents, resulting in improved system reliability and less downtime for maintenance
  2. More consistent nutrient delivery to the plants, promoting healthier growth and higher yields
  3. Lower costs associated with replacing clogged emitters and other affected irrigation components
  4. Increased efficiency in fertilizer use, as fewer nutrients were lost to precipitation

Case Study 3: Resolving Biofilm Clogs with Monitoring and Targeted Treatment

The Problem

A hydroponic grower noticed an unusual trend on his AROYA dashboard for several irrigation zones. The water content percentage (WC%) and substrate EC levels were deviating from their expected patterns, despite no changes being made to the irrigation programming. Additionally, the grower observed that the volume of feed captured in the zone feed cups was consistently lower than the calculated irrigation volume.

Suspecting an issue with the irrigation system, the grower inspected the filtration components and discovered significant biofilm accumulation on the filters and membranes. Upon further investigation, he realized that the filters had exceeded their recommended replacement date, allowing the biofilm to proliferate and cause clogs throughout the system.

The Solution

To address the biofilm clog issue, the grower implemented a two-step approach:

  1. Targeted treatment: The grower used Bioflo, Front Row Ag’s enzymatic cleaner, to soak the affected irrigation zones. Bioflo is designed to break down and remove biofilm accumulation, effectively clearing the clogs and restoring proper flow through the system.
  2. System renovation: After treating the system with Bioflo, the grower thoroughly flushed the irrigation lines (first through the flush valves) with fresh water to remove any remaining debris and cleaning solution. He then replaced the outdated filters and membranes with new ones to prevent the rapid reoccurrence of biofilm accumulation.

By combining targeted treatment and system renovation, the grower successfully eliminated the biofilm clogs and restored the irrigation system's performance.

The Outcome

The resolution of the biofilm clog issue led to several benefits:

  1. Improved system performance: With the clogs removed and the filters replaced, the irrigation system regained its optimal flow rates and uniform water distribution. The WC% and substrate EC levels returned to their expected patterns on the AROYA dashboard.
  2. Increased crop health and yield: As the plants received consistent and adequate water and nutrient delivery, they experienced healthier growth and improved yield.
  3. Enhanced system longevity: By addressing the biofilm accumulation and replacing the worn components, the grower extended the lifespan of the irrigation system and reduced the risk of future clogs.
  4. Proactive maintenance: The experience reinforced the importance of regular system monitoring and adhering to recommended replacement schedules for filters and membranes.


Clogs in hydroponic irrigation systems can significantly impact plant health, system efficiency, and overall growing success. Uneven nutrient distribution, water stress, root zone hypoxia, decreased yields, and damage to system components are just a few of the consequences of untreated clogs.

To minimize the risk of clogs and ensure optimal system performance, hydroponic growers must prioritize clog prevention and promptly address any issues that arise. This can be achieved through a comprehensive strategy that includes:

  1. Proper system design
  2. Regular maintenance
  3. Water treatment
  4. Effective monitoring

Establishing a routine monitoring schedule and performing regular maintenance tasks are crucial for early detection and timely intervention. Keeping detailed records of maintenance activities and system performance can help growers identify trends and make informed decisions.

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